9A84 | pdb_00009a84

52-mer bacterial gasdermin pore model from Vitiosangium sp.

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.


Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 1 
  • Representative Model: 1 

This is version 1.0 of the entry. See complete history


Literature

Structure and assembly of a bacterial gasdermin pore

Johnson, A.G.Mayer, M.L.Schaefer, S.L.McNamara-Bordewick, N.K.Hummer, G.Kranzusch, P.J.

(2024) Nature 

  • DOI: https://doi.org/10.1038/s41586-024-07216-3
  • Primary Citation of Related Structures:  
    8SL0, 9A84, 9A85, 9A86

  • PubMed Abstract: 

    In response to pathogen infection, gasdermin (GSDM) proteins form membrane pores that induce a host cell death process called pyroptosis 1-3 . Studies of human and mouse GSDM pores have revealed the functions and architectures of assemblies comprising 24 to 33 protomers 4-9 , but the mechanism and evolutionary origin of membrane targeting and GSDM pore formation remain unknown. Here we determine a structure of a bacterial GSDM (bGSDM) pore and define a conserved mechanism of pore assembly. Engineering a panel of bGSDMs for site-specific proteolytic activation, we demonstrate that diverse bGSDMs form distinct pore sizes that range from smaller mammalian-like assemblies to exceptionally large pores containing more than 50 protomers. We determine a cryo-electron microscopy structure of a Vitiosangium bGSDM in an active 'slinky'-like oligomeric conformation and analyse bGSDM pores in a native lipid environment to create an atomic-level model of a full 52-mer bGSDM pore. Combining our structural analysis with molecular dynamics simulations and cellular assays, our results support a stepwise model of GSDM pore assembly and suggest that a covalently bound palmitoyl can leave a hydrophobic sheath and insert into the membrane before formation of the membrane-spanning β-strand regions. These results reveal the diversity of GSDM pores found in nature and explain the function of an ancient post-translational modification in enabling programmed host cell death.


  • Organizational Affiliation
    • Department of Microbiology, Harvard Medical School, Boston, MA, USA. algejohnson@gmail.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gasdermin bGSDM234Vitiosangium sp. (strain GDMCC 1.1324)Mutation(s): 0 
Gene Names: DAT35_31115
UniProt
Find proteins for A0A2T4VDM4 (Vitiosangium sp. (strain GDMCC 1.1324))
Explore A0A2T4VDM4 
Go to UniProtKB:  A0A2T4VDM4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2T4VDM4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
P1L
Query on P1L
A
AA [auth a]
B
BA [auth b]
C
A,
AA [auth a],
B,
BA [auth b],
C,
CA [auth c],
D,
DA [auth d],
E,
EA [auth e],
F,
FA [auth f],
G,
GA [auth g],
H,
HA [auth h],
I,
IA [auth i],
J,
JA [auth j],
K,
KA [auth k],
L,
LA [auth l],
M,
MA [auth m],
N,
NA [auth n],
O,
OA [auth o],
P,
PA [auth p],
Q,
QA [auth q],
R,
RA [auth r],
S,
SA [auth s],
T,
TA [auth t],
U,
UA [auth u],
V,
VA [auth v],
W,
WA [auth w],
X,
XA [auth x],
Y,
YA [auth y],
Z,
ZA [auth z]
L-PEPTIDE LINKINGC19 H37 N O3 SCYS
Experimental Data & Validation

Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 1 
  • Representative Model: 1 

Structure Validation

View Full Validation Report

View Summary Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-22
    Type: Initial release